Hi, Sorry I was swamped recently. But yeah, we can even create an extended type system to store these items temporarily and add them into the main/core type system afterwards. There was an existing item to upgrade UIMA, but agreed- it will require much more testing. If it works, we can upgrade it in our sandbox area or create a branch if necessary.
—Pei > On Jan 18, 2016, at 9:06 AM, Peter Klügl <peter.klu...@averbis.com> wrote: > > Hi, > > a new patch is attached. > > @Pei: > are there suitable annotation types in the cTAKES type system? Some > project in cTAKES uses something like OntologyMatch... I map it to > IdentifiedAnnotation right now, but there are many empty features... > > @Azad: > I changed the rules a bit, especially the capitalization like I use it > in ruta normally. The wordlist are compiled to a trie by the maven > plugin. I also added the two regexes for url and email. I extended the > regex for the url. I also changed the evaluation order of some rules > (with @). Feel free to add simple examples to examples.csv for the unit > tests. > > Let me know if you need more information about the changes. > > Do you wanna have help with the other rule sets? Or should we split them up? > > Best, > > Peter > > Am 18.01.2016 um 11:04 schrieb Peter Klügl: >> Hi, >> >> great. I will integrate them in the project and in the next patch. >> >> Best, >> >> Peter >> >> Am 18.01.2016 um 00:58 schrieb Azad Dehghan: >>> Three NERs translated and uploaded. >>> >>> PS. I will validate all NERs once we have them all completed. >>> >>> Cheers, >>> Azad >>> >>> On 24 November 2015 at 10:37, Azad Dehghan <azad.dehg...@gmail.com> wrote: >>> >>>> This is on my todo list for Dec. as well. If there are any more volunteers >>>> for translating JAPE to RUTA, please get in touch. >>>> >>>> Cheers, >>>> Azad >>>> >>>> On 24 Nov 2015 09:55, "Peter Klügl" <peter.klu...@averbis.com> wrote: >>>>> Hi, >>>>> >>>>> I just wanted to mention that I haven't forgot about it. Unfortunately, >>>>> there is just no spare time right now. I hope I will be able to provide >>>>> the patches in December. >>>>> >>>>> Best, >>>>> >>>>> Peter >>>>> >>>>> Am 06.11.2015 um 16:40 schrieb Pei Chen: >>>>>> Hi Peter, >>>>>> I think the ctakes-examples is probably a good starting point at least >>>>>> in terms of maven modules, etc. I think it would be good if we use >>>>>> uimaFIT style as primary approach to wiring components together and >>>>>> generate desc's as secondary... >>>>>> I think the actual components that would be required is probably best >>>>>> left up to what is actually required for best performing c-deid. The >>>>>> output would be interesting, I'm not sure if we should treat this as >>>>>> an independent preprocessing component or part of a pipeline (in which >>>>>> case, we may need to propose a change to the type system or perhaps an >>>>>> alternative JCas view. You can probably open up that discussion to >>>>>> the dev group as you see fit.) >>>>>> >>>>>> My 2 cents... >>>>>> >>>>>> >>>>>> On Fri, Nov 6, 2015 at 3:38 AM, Peter Klügl <peter.klu...@averbis.com> >>>> wrote: >>>>>>> Hi, >>>>>>> >>>>>>> Is there a cTAKES project that may serve as an example on how the >>>> cTAKES >>>>>>> community develops or how a project should look like? >>>>>>> I learned that different people set up UIMA project in a quite >>>> different >>>>>>> manner and I do not what to get inspired by "some sort of out-dated" >>>>>>> approach in the cTAKES repo. >>>>>>> >>>>>>> Are there restriction or preferences about the preprocessing >>>> components >>>>>>> that should be used and the kind of "output" of the project. >>>>>>> Components: On which components may the componetns rely: tokenizer, >>>> ... >>>>>>> parser, ... dict lookup? >>>>>>> "output": Should the project provide a pipeline or a single AE? >>>>>>> >>>>>>> More comments below. >>>>>>> >>>>>>> Am 03.11.2015 um 16:54 schrieb Azad Dehghan: >>>>>>>>> Who else plans to provide patches for it? Just to avoid duplicate >>>> work >>>>>>>>> and to coordnate the efforts ... >>>>>>>>> >>>>>>>> I would like to help with the translating JAPE to RUTA. >>>>>>> You can already go ahead with the UIMA Ruta Workbench if you want, or >>>>>>> wait until I set up the project with ruta integration. >>>>>>> >>>>>>> If any questions arise, just ask :-) >>>>>>> >>>>>>>>> Is there a development dataset which was utilized for the initial >>>>>>>>> development, and if yes, is it possible to contribute it too? >>>>>>>>> >>>>>>>> The data set is unfortunately not publicly available; i2b2 >>>>>>>> <https://www.i2b2.org/NLP/DataSets/Main.php> typically releases the >>>> data >>>>>>>> sets 12 months after a given challenge; this is done on an >>>> individual basis >>>>>>>> and involve a Data Use Agreement. >>>>>>>> >>>>>>>> However, I will be able to conduct and coordinate the validation. >>>>>>>> >>>>>>> Ok, I'll investigate if we have already access to the dataset here. >>>>>>> >>>>>>> >>>>>>>>> My first step would be: >>>>>>>>> - set up a maven project >>>>>>>>> - set up a development pipeline in a test (with cTAKES components >>>>>>>>> replacing the previous ANNIE preprocessing) >>>>>>>>> >>>>>>>>> >>>>>>>>> But one item that we need to review is the 3rd party libs jars that >>>>>>>>> were included to ensure compatibility. I’ll be sure to take a look >>>> at >>>>>>>>> that over the next few weeks. >>>>>>>>> >>>>>>>>> —Pei >>>>>>>>> >>>>>>>>> >>>>>>>> @Pei - once ANNIE components are replaced there is should not be a >>>> need to >>>>>>>> worry about the 3rd party libs. >>>>>>>> >>>>>>>> Also, just a thought: we may want to create an independent component >>>> for >>>>>>>> the Two Pass recognition (TwoPass.java) as this method have shown >>>> useful >>>>>>>> for general NER on longitudinal data and surely useful independent >>>> of the >>>>>>>> deid component. >>>>>>>> >>>>>>>> >>>>>>>> Cheers, >>>>>>>> Azad >>>>>>>> >
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